biogems.info

New: CloudBioLinux packages are now listed on biogems.info !

#	biogem	description	by	version	released	stars	issues	total	90d*)	7d	90d**)
								downloads		commits
1	bio	Bioinformatics library (...)	BioRuby project	1.4.3.0001	6 months	30	18	52655	5106
2	biodiversity	Parser of scientific names (...)	Dmitry Mozzherin	3.1.2	5 months	10	5	27876	3506	0	0
3	bio gem	Biogem is a software generator for Ruby in (...)	Raoul J.P. Bonnal, Pjotr Prins	1.3.5	4 months	14	11	23921	2730
4	bio samtools	Binder of samtools for Ruby, on the top (...)	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	0.6.0	12 months	14	4	18614	2214	0	3
5	entrez	Http requests to entrez e-utilities (...)	Jared Ning	0.5.8.1	2 years	4	...	15480	1572	0	0
6	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome (...)	Hiroyuki Mishima, Jan Aerts	0.5.3	3 months	13	1	14105	1853	7	7
7	intermine	Webservice client library for intermine data-warehouses (...)	Alex Kalderimis	1.04.00	5 months			13755	1794
8	bio gff3	Gff3 parser for big data (...)	Pjotr Prins	0.9.1	15 months	6	2	12377	1275
9	sequenceserver	Blast search made easy! (...)	Anurag Priyam, Ben J Woodcroft, Yannick Wurm	0.8.6	1 week	30	30	11523	1765
10	bio gadget	Gadgets for bioinformatics (...)	Shintaro Katayama	0.4.8	6 months		...	10774	2753
11	bio maf	Maf parser for BioRuby (...)	Clayton Wheeler	1.0.1	16 months	9	29	9942	1760	0	0
12	bio logger	Log4r wrapper with extra features for roles and (...)	Pjotr Prins	1.0.1	20 months	4	2	9057	820	0	0
13	bio grid	A biogem to submit jobs on a queue (...)	Francesco Strozzi	0.3.3	13 months	5	...	8198	1470	0	0
14	bio blastxmlparser	Very fast blast xml parser and library for (...)	Pjotr Prins	1.1.1	10 months	9	...	7005	878	0	0
15	bio faster	A fast parser for fastq files (...)	Francesco Strozzi	0.4.5	18 months	9	...	6731	886	0	0
16	bio svgenes	Create pretty svg-format images of features, gene models (...)	Dan MacLean	0.3.3	6 months	6	5	6606	1685
17	bio alignment	Support for multiple sequence alignments (msa) (...)	Pjotr Prins	0.0.7	17 months	6	4	6295	803	0	0
18	bio phyta	Pipeline to remove contaminations from est libraries (...)	Philipp Comans	0.9.4	2 years	1	...	6184	634
19	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha (...)	George Githinji	0.7.1	9 months	1	...	5699	743
20	scaffolder	Build genome output files (...)	Michael Barton	0.5.0	4 months		...	5667	621
21	bio assembly	BioRuby assembly plugin (...)	Chase Miller, Francesco Strozzi	0.1.0	2 years	4	...	5494	521
22	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv (...)	Pjotr Prins	0.8.0	13 months	7	19	5310	953
23	genfrag	This is a development release (...)	Pjotr Prins and Trevor Wennblom	0.0.0.4	4 years			5250	396
24	bio bigbio	Low memory sequence emitters (...)	Pjotr Prins	0.1.5	7 months	6	1	5198	636	0	1
25	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org) (...)	Rutger Vos, Anurag Priyam	1.1.0	19 months	6	1	5109	533	0	0
26	eutils	Lightweight Ruby api for ncbi eutils (...)	Joon Lee, aka seouri	0.2.1	5 months	6	...	4969	534
27	bio graphics	Library for visualizing genomic regions (...)	Jan Aerts	1.4	5 years			4939	404
28	bio signalp	A wrapper for the signal peptide prediction algorith (...)	Ben J Woodcroft	0.3.0	15 months	1	...	4866	668	0	0
29	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point (...)	George Githinji, Pascal Betz	0.1.3	21 months	3	...	4838	538
30	bio tm hmm	A BioRuby plugin for interaction with the transmembrane (...)	Ben J. Woodcroft	0.2.2	12 months	2	...	4773	675	0	0
31	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps (...)	Hiroyuki Mishima	0.1.2	2 years	3	...	4498	439
32	bio sambamba	Ruby wrapper for sambamba tool (...)	Artem Tarasov	0.0.5	15 months	2	...	4437	681
33	bio octopus	Running and parsing of the protein transmembrane domain (...)	Ben J Woodcroft	0.1.1	2 years	1	...	4306	409
34	bio ngs	Bio-ngs provides a framework for handling ngs data (...)	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	18 months	26	14	4253	416	0	0
35	bio kmer counter	A biogem for counting small kmers for fingerprinting (...)	Ben J Woodcroft	0.1.2	6 months	5	...	3897	778
36	goruby	Gene ontology (go) interface for Ruby (...)	Ben J Woodcroft	0.2.0	3 years	7	...	3838	301	0	0
37	biointerchange	An open source framework for transforming heterogeneous data (...)	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.1	3 months	7	3	3725	1062	0	6
38	ruby ensembl api	Api to ensembl databases (...)	Jan Aerts, Francesco Strozzi	1.0.1	2 years	30	4	3599	279
39	bio bwa	Ruby binding for bwa mapping software (...)	Francesco Strozzi	0.2.2	2 years	3	...	3544	382
40	bio lazyblastxml	A plugin that allows you to parse large (...)	robsyme	0.4.0	2 years	1	...	3402	399
41	bio pileup iterator	Iterate through a samtools pileup file (...)	Ben J. Woodcroft	0.0.4	12 months	1	...	3199	420	0	0
42	bio bgzf	Reading/writing bgzf blocks (...)	Artem Tarasov, Clayton Wheeler	0.2.1	16 months	1	...	3191	537	0	0
43	bio kb illumina	Geneexpression illuminahumanannotation (...)	Raoul J.P. Bonnal	0.1.0	2 years	1	...	2846	272	0	0
44	bio plasmoap	Implementation of the plasmoap algorithm (...)	Ben J Woodcroft	0.0.2	23 months	1	...	2827	296	0	0
45	bio band	Data mining algorithms for jRuby (...)	arrigonialberto86	0.1.11	2 months	9	3	2662	2163
46	bio cd hit report	Read and manipulate cd-hit clusters (...)	George Githinji	0.1.0	7 months	2	...	2570	547	0	0
47	bio publisci	Publish scientific results to the semantic web (...)	Will Strinz	0.1.0	11 weeks		...	2490	1416
48	bio rdf	Bioinformatics triple-store support (...)	Pjotr Prins	0.0.2	18 months	4	1	2488	292	5	65
49	bio affy	Parse affymetrix cel/cdf files (...)	Pjotr Prins	0.5.1	2 years	2	1	2432	288
50	bio gff3 pltools	Ruby wrapper for the gff3-pltools (...)	Marjan Povolni	0.3.0	16 months			2389	395
51	bio chembl	Chembl rest api client, parser and container (...)	Mitsuteru Nakao	0.1.3	16 months	1	1	2326	386	0	0
52	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser, (...)	Raoul J.P. Bonnal	0.0.1	2 years	1	...	2312	288	0	0
53	bio ucsc util	Ruby binding to the ucsc kent utilities (...)	throwern	0.1.2	14 months	1	...	2298	449	0	0
54	bio gngm	Next-generation mapping of mutations (...)	Dan MacLean	0.2.1	12 months	1	...	2289	404	0	0
55	bio tabix	Ruby binding for samtools tabix (...)	throwern	1.0.1	10 weeks	3	...	2226	698
56	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal (...)	Ben J. Woodcroft	0.3.0	19 months	1	...	2142	269
57	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be (...)	Ben J Woodcroft	0.0.3	22 months	1	...	2099	280
58	bio hmmer model	Parse pfam hmm definition files (...)	Ben J. Woodcroft	0.0.2	18 months	1	...	1761	271	0	0
59	bio protparam	A protparam compatible utility for BioRuby (...)	hryk	0.2.0	11 months	1	...	1693	485
60	bio gag	Bio-gag is a biogem for detecting and correcting (...)	Ben J Woodcroft	0.1.0	13 months	3	...	1568	272
61	bio unichem	BioRuby plugin for unichem rest web service (...)	Mitsuteru Nakao	0.3.0	10 months		...	1535	429
62	bio basespace sdk	Basespace Ruby sdk is a Ruby based software (...)	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	4 months	7	2	1479	747	0	4
63	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns (...)	Trevor Wennblom	1.0.0	2 years		1	1478	151
64	bio sge	BioRuby plugin for sun grid engine (...)	Toshiaki Katayama	0.0.0	2 years	4	...	1475	153	0	0
65	bio hello	Hello world plugin for the BioRuby (just for (...)	Toshiaki Katayama	0.0.0	2 years	3	...	1464	158
66	dna sequence aligner	Does high pairwise alignment of sequencing reads with (...)	John T. Prince	0.0.2	3 years			1456	141
67	bio synreport	Reports whether a nucleotide change results in synonymous (...)	Dan MacLean	0.1.2	6 months		...	1407	431
68	bio krona	This biogem is built around krona, a flashy (...)	Ben J. Woodcroft	0.1.1	3 months	1	...	1370	447
69	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of (...)	Ben J Woodcroft	0.1.0	2 years	1	...	1228	139	0	0
70	bio core ext	BioRuby core ext: plugins which require external library (...)	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	2 years	1	...	1205	162
71	bio data restriction enzyme	Restriction enzyme dataset (...)	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	2 years		...	1164	148
72	bio biolinux	Meta package for biolinux distribution (...)	Raoul J.P. Bonnal	0.1.0	2 years	2	...	1160	155
73	bio foo	One-line summary of your gem (...)	Toshiaki Katayama	0.0.0	2 years	1	...	1154	152
74	bio ensembl	A Ruby api to the ensembl database (...)	Jan Aerts, Francesco Strozzi	1.1.0	2 years	3	...	1148	151
75	bio dbsnp	Decoding the dbsnp bitfield (...)	Hiroyuki Mishima	0.1.1	2 years	2	...	1128	143
76	bio phyloxml	Phyloxml plugin for BioRuby (...)	Diana Jaunzeikare, Clayton Wheeler	0.9.0	18 months	3	...	1110	141	0	0
77	bio exportpred	Wrapper around the exportpred algorithm for predicting p (...)	Ben J Woodcroft	0.0.1	22 months	1	...	1085	157
78	bio aliphatic index	A simple biogem that allows computation of the (...)	Ben J Woodcroft	0.0.1	22 months	1	...	1079	142
79	bio hydropathy	Hydropathy scale for BioRuby (...)	Ben J Woodcroft	0.0.1	22 months	1	...	1062	139	0	0
80	intermine bio	Biological extensions for the intermine webservice client library (...)	Alex Kalderimis	0.98.1	2 years			998	111
81	bio statsample timeseries	Timeseries modules for statsample (...)	Ankur Goel, Claudio Bustos	0.2.1	11 weeks		...	993	793
82	bio hmmer3 report	Enables parsing of hmmer version 3 reports (...)	Christian Zmasek, Ben J Woodcroft	0.0.1	19 months	1	1	936	146	0	0
83	bio incanter	Build graph with jRuby (...)	Matteo Picciolini	0.1.0	16 months		...	861	154
84	bio ipcress	A programmatic interface to the ipcress in-silico pcr (...)	Ben J Woodcroft	0.0.1	16 months	1	...	824	158	0	0
85	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata (...)	Ben J. Woodcroft	0.0.1	11 months		...	611	160	0	0
86	bio gggenome	Gggenome Ruby client (...)	Mitsuteru Nakao	0.2.0	3 months	1	...	574	340
87	bio ensembl rest	Ruby ensembl rest api (...)	Alberto Donizetti	0.2.0	10 weeks	2	...	483	401	0	7
88	bio statsample glm	Generalized linear models for statsample (...)	Ankur Goel	0.1.1	11 weeks		...	451	451
89	bio stockholm	Parse stockholm sequence alignment format (...)	Ben J. Woodcroft	0.0.1	5 months		...	374	161	0	0
90	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood (...)	Fernando Izquierdo	0.1.0	4 months		...	328	165
91	bio qtlHD	(...) pre		pre				279	19

*) gem downloads (total & last 90 days) from rubygems.org as of 2013-12-09
**) number of commits on GitHub (last 7 days & last 90 days)